Net Interest Income and Net Interest Margin
Net interest income for the third quarter increased $0.5 million to $13.8 million from $13.3 million in the linked quarter, and increased $1.5 million from the prior year quarter. The increase in the linked quarter was driven by an increase in interest income coupled with a decrease in interest expense. The increase from the prior year quarter was all driven by a decrease in interest expense. Included in net interest income in the third quarter was $0.4 million of loan fees related to the PPP. Net interest margin, on a tax equivalent basis, was 3.50% for the third quarter, an increase from 3.46% in the linked quarter, and a reduction from 3.64% in the third quarter of 2019.
Loans
Loans held for investment totaled $1.3 billion at September 30, 2020, decreasing $1.5 million or 0.1% from the linked quarter and increasing $130 million or 11.3% from the prior year quarter. Growth in loans over the prior year quarter was primarily due to an increase in commercial loans for customers who participated in the PPP. Non-performing loans to total loans was 0.45% at September 30, 2020, and 0.70% and 0.41% at the end of the linked quarter and prior year quarter, respectively.
The yield earned on average loans held for investment was 4.66% for the third quarter, compared to 4.68% for the linked quarter and 5.13% for the prior year quarter.
In April 2020, the Company began offering loans through the PPP which was part of the CARES Act passed by Congress. At September 30, 2020, it had provided over 1,275 loans to small business customers totaling $88.4 million, for an average of $69,200 per loan.
As provided for by the CARES Act, the Company has also offered payment modifications to borrowers. Disaster relief payment modifications granted to-date include approximately 578 loans totaling $303.2 million. At September 30, 2020, 42 loans totaling $91.1 million or 7.1% of total loans remained in some form of a modification. These loan modifications include $44.6 million or 48.9% on interest only, and $46.5 million or 51.1% on full deferral. (See table below titled Loan Modifications under the CARES Act by NAICS Code.)
Asset Quality
Non-performing loans totaled $5.8 million at September 30, 2020, a decrease of $3.1 million from $8.9 million at the end of the linked quarter, primarily due to one loan relationship that was paid off during the quarter. In the third quarter 2020, the Company had net loan charge-offs of $58,000 compared to net loan recoveries of $29,000 in the linked quarter, and $155,000 of net loan charge-offs in the prior year quarter.
The Company recorded a provision for credit losses of $1.2 million for the third quarter 2020 compared to $0.9 million for the linked quarter and $0.5 million for the third quarter 2019. The increase in the allowance for loan losses in the current quarter and linked quarter compared to the prior year quarter is primarily due to the additional loan loss provision of $0.8 million and $0.6 million, respectively, for the COVID-19 pandemic as previously described above.
The allowance for loan losses at September 30, 2020, was $17.8 million, or 1.39% of outstanding loans, and 305.5% of non-performing loans. At June 30, 2020, the allowance for loan losses was $16.6 million, or 1.30% of outstanding loans, and 186.6% of non-performing loans. At September